Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Phosphoproteomic analysis of calcium signaling

ABSTRACT: Calcium signaling plays a pivotal role in t cell activation through activation of kinases and phosphatases, but comprehensive analysis to overview calcium-induced phosphorylation has never been performed. To investigate Ca2+-mediated phosphorylation globally, we next undertook a phosphoproteomic analysis of calcium signaling, especially focused on the Ca2+-dependent phosphatase, calcineurin. Normal mouse thymocytes were stimulated in 4 different conditions; 1). DMSO, 2). CsA, 3). IOM, or 4). CsA and IOM, and compared their phosphorylation status.

INSTRUMENT(S): QSTAR

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Primary Cell, T Cell

SUBMITTER: Atsushi Hatano

LAB HEAD: Keiichi I. Nakayama

PROVIDER: PXD000973 | Pride | 2022-02-22

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20111105_CsA_iTRAQ_01.mgf	Mgf
	20111105_CsA_iTRAQ_01.pride.mgf.gz	Mgf
	20111121_CsA_iTRAQ_Fr1_2.mgf	Mgf
	20111121_CsA_iTRAQ_Fr1_2.pride.mgf.gz	Mgf
	20111122_CsA_iTRAQ_Fr3.mgf	Mgf

Items per page:

1 - 5 of 35

Publications

Phosphoproteomics analyses show subnetwork systems in T-cell receptor signaling.

Hatano Atsushi A Matsumoto Masaki M Nakayama Keiichi I KI

Genes to cells : devoted to molecular & cellular mechanisms 20160907 10

A key issue in the study of signal transduction is how multiple signaling pathways are systematically integrated into the cell. We have now performed multiple phosphoproteomics analyses focused on the dynamics of the T-cell receptor (TCR) signaling network and its subsystem mediated by the Ca<sup>2+</sup> signaling pathway. Integration of these phosphoproteomics data sets and extraction of components of the TCR signaling network dependent on Ca<sup>2+</sup> signaling showed unexpected phosphoryl ...[more]

PMID: 27600695

Similar Datasets

Phosphoproteomic analysis of TCR signaling with inhibitors

Project description:MAPK-Erk and calcium-Calcineurin pathways are major signaling pathways activated during TCR signal transduction. We investigated the effect of these signaling pathway with the use of selective inhibitors of Mek and calcineurin.

2022-02-22 | PXD000972 | Pride

Quantitative phosphoproteomic analysis of TCR signaling

Project description:To define the physiological properties of TCR signaling, We investigated the global dynamic view of TCR-dependent phosphorylation with the use of thymocytes stimulated with antibodies to CD3 to mimic TCR activation

2022-02-22 | PXD000969 | Pride

Noncanonical pathway for regulation of CCL2 expression by an mTORC1-FOXK1 axis promotes recruitment of tumor-associated macrophages

Project description:C-C chemokine ligand 2 (CCL2) plays pivotal roles in tumor formation, progression, and metastasis. Although CCL2 expression has been found to be dependent on the nuclear factor (NF)–κB signaling pathway, the regulation of CCL2 production in tumor cells has remained unclear. Mammalian target of rapamycin complex 1 (mTORC1) is a protein kinase that is activated in various tumor cell types. We have now identified a noncanonical pathway for regulation of CCL2 production that is mediated by mTORC1 but independent of NF-κB. Multiple phosphoproteomics approaches identified the transcription factor forkhead box K1 (FOXK1) as a downstream target of mTORC1, with dephosphorylation of FOXK1 in response to mTORC1 activation resulting in transactivation of the CCL2 gene. Inhibition of the mTORC1-FOXK1 axis attenuated insulin-induced CCL2 production as well as the accumulation of tumor-associated monocytes-macrophages and tumor progression in mice. Our results suggest that FOXK1 directly links mTORC1 signaling and CCL2 expression in a manner independent of NF-κB, and that CCL2 produced by this pathway contributes to tumor progression. Specific inhibition of FOXK1 may thus be a potential therapeutic strategy for cancer.

2017-11-30 | PXD007996 | Pride

Comparative analysis of the human and mouse placental transcriptome and proteome

Project description:An important question for the use of the mouse as a model for studying human disease is the degree of functional conservation of genetic control pathways from human to mouse. The human and mouse placenta show structural similarities but there have been no systematic attempt to assess their molecular similarities or differences. We built a comprehensive database of protein and microarray data for the highly vascular exchange region micro-dissected from the human and mouse placenta near-term. Abnormalities in this region are associated with two of the most common and serious complications of human pregnancy, maternal preeclampsia (PE) and fetal intrauterine growth restriction (IUGR), each disorder affecting ~5% of all pregnancies. Over 7,000 orthologs were detected with 70% co-expressed and over 80% of genes known to cause placental phenotypes in mouse were co-expressed. These genes form a tight protein-protein interaction network with novel candidate genes likely to be important in placental structure and/or function. The entire data is available as a web-accessible database to guide the informed development of mouse models to study human disease This experiment is now fully represented in NCBI Peptidome database with accession PSE115; http://www.ncbi.nlm.nih.gov/peptidome/search/index.shtml?acc=PSE115 Microdissection of human villous trees and mouse placental labyrinth. Tissues were split for microarray and protein analysis. For protein analysis samples were first fractionated by differential sucrose gradients into mitochrondria, cytosol, microsomes and nuclei. Mitochrondira and neuclei were each extracted by two different methods for soluble and insoluble material. Each subcellular fraction for each tissue was analysed in quintuplet by 9 step 2 dimensional LC/MSMS. This generated a total of 270 mzXML files for each tissue.

2009-06-29 | E-GEOD-13299 | biostudies-arrayexpress

A calcium-induced signaling cascade leading to osteogenic differentiation of human bone marrow-derived mesenchymal stromal cells

Project description:The response of osteoprogenitors to calcium (Ca2+) is of primary interest for both normal bone homeostasis and the clinical field of bone regeneration. The latter makes use of calcium phosphate-based bone void fillers to heal bone defects, but it is currently not known how Ca2+ released from these ceramic materials influences cells in situ. Here, we have created an in vitro environment with high extracellular Ca2+ concentration and investigated the response of human bone marrow-derived mesenchymal stromal cells (hMSCs) to it. Ca2+ enhanced proliferation and morphological changes in hMSCs. Moreover, the expression of osteogenic genes is highly increased. A 3-fold up-regulation of BMP-2 is observed after only 6 h and pharmaceutical interference with a number of proteins involved in Ca2+ sensing showed that not the calcium sensing receptor, but rather type L voltage-gated calcium channels are involved in mediating the signaling pathway between extracellular Ca2+ and BMP-2 expression. MEK1/2 activity is essential for the effect of Ca2+ and using microarray analysis, we have identified c-Fos as an early Ca2+ response gene. We have demonstrated that hMSC osteogenesis can be induced via extracellular Ca2+, a simple and economic way of priming hMSCs for bone tissue engineering applications. For more information check: https://cbit.maastrichtuniversity.nl/

2018-10-06 | E-MTAB-7222 | biostudies-arrayexpress

Expression profiling of ncRNAs with custom microarray of CaV 1.3 knockout mice compared to wild type mice

Project description:For screening mouse models for CNS diseases for changes in ncRNA expression, we first investigated two models with impaired voltage-gated Ca2+ channel activity, i.e. the lethargic mutant of the auxiliary calcium channel β4 subunit (Cacnb4lh; (Burgess et al. 1997)) and knockout mice for the L-type calcium channel CaV1.3 (Platzer et al. 2000), which have been implicated in a variety of neurological disorders such as psychiatric disorders (Cacnb4) or Parkinsons disease (Cav1.3).

2014-10-31 | E-MTAB-2742 | biostudies-arrayexpress

Expression profiling of ncRNAs with custom microarray of lethargic Cacnb4 mutant mice compared to wild type mice

2014-10-31 | E-MTAB-2750 | biostudies-arrayexpress

Discrimination of dormant and active hematopoietic stem cells by G0 markers reveals dormancy regulation by cytoplasmic calcium

Project description:High-throughput small molecule screening revealed that high concentrations of cytoplasmic calcium ([Ca2+]c) were linked to dormancy of HSCs.To clarify molecular difference between [Ca2+]chigh and [Ca2+]clow cells, we performed RNA-Seq analysis using [Ca2+]chigh and [Ca2+]clow cells.

2019-12-20 | GSE138884 | GEO

Cytosolic calcium and nuclear calcium-regulated transcription networks in response to ABA and JA

Project description:Calcium acts as a universal second messenger to regulate gene expression in both developmental processes and responses to environmental stresses. Previous studies showed that a number of stimuli can induce calcium increases in the cytoplasm and nucleus, independently. However, the gene expression network deciphering [Ca2+]cyt and/or [Ca2+]nuc signaling pathway remain obscure. Using transgenic Arabidopsis containing a fusion protein, comprising rat parvalbumin (PV) with either a nuclear export sequence (PV-NES) or a nuclear localization sequence (NLS-PV), to selectively buffer the cytosolic or nucleosolic calcium, we identified the [Ca2+]cyt- or /and [Ca2+]nuc-regulated ABA- and MeJA-responsible genes with the Arabidopsis Genome Oligo array.

2018-01-25 | GSE109611 | GEO

Calcium deficient transcriptome analysis of rice

Project description:Calcium is an essential macronutrient and plant requires it in large amounts for normal growth and development. This ion participated in innumerable processes and affects nearly all aspects of plant growth and development such as signal transduction, metabolism of lipids, proteins, and carbohydrates, cell growth, cell wall and membrane stabilization. We used whole genome microarrays to determine the transcriptomic profile of rice seedlings exposed to short-term and long term Ca2+ deficiency followed by Ca2+ resupply. Calcium treated seedlings were used for for RNA extraction and hybridization on Agilent microarray platform. Three biological replicates of each sample were used for microarray analysis. We wanted to know the altered expression patterns of calcium-responsive genes majorly involved in metabolic processes, signal transdction pathways, transcriptional regulation, and transport of multiple molecules including Ca2+. Seeds of indica rice were surface sterilized and grown hydroponically in rice growing medium. Plants were grown in the rice growth room under the condition of 16 h light/8 h dark (28M-BM-0C) photoperiod with 70 % humidity. After 5 days of normal growth, some of the seedlings were transferred to nutrient solution lacking CaCl2 (-Ca2+). After 5 and 14 days, calcium (0.798 mM CaCl2) was resupplied to the plants grown in -Ca2+ medium for 6 h.

2014-01-17 | E-GEOD-50917 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data